filament

We have developed a novel approach, named DF-Tracing, to tackle this challenge. This method first extracts the neurite signal (foreground) from a noisy image by using anisotropic filtering and automated thresholding. Then, DF-Tracing executes a coupled distance-field (DF) algorithm on the extracted foreground neurite signal and reconstructs the neuron morphology automatically. Two distance-transform based “force” fields are used: one for “pressure”, which is the distance transform field of foreground pixels (voxels) to the background, and another for “thrust”, which is the distance transform field of the foreground pixels to an automatically determined seed point. The coupling of these two force fields can“push” a “rolling ball” quickly along the skeleton of a neuron, reconstructing the 3D cell morphology.

The ultimate goal of the NET framework is to make images of networks processable by computers. Therefore we want to have a pixel based image as input, as output we want a representation of the network visible in the image that retains as much information about the original network as possible. NET achives this by first segmenting the image and then vectorizing the network and then extracting information. The information we extract is

• First and foremost the graph of the network. We find the crossings (nodes) and connections between crossings (edges) and therefore extract information about the neighborhood relations, the topology of the network.
• We also extract the coordinates of all nodes which enables us to embed them into space. We therefore extract information about the geometry of the network.
• Last but not least we track the radii of the edges in the extraction process. Therefore every edge has a radius which can be identified with its conductivity.

In the following we will first provide detailed instructions on how to install NET on several platforms. Then we describe the functionality and options of each of the four scripts that make up the NET framework.

ORION: Online Reconstruction and functional Imaging Of Neurons: segmentation and tracing of neurons for reconstruction.

A project to develop tools that explore single neuron function via sophisticated image analysis. ORION software bridges advanced optical imaging and compartmental modeling of neuronal function by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function. The goal of this project is to develop a computational and experimental framework to allow real-time mapping of functional imaging data (e.g., spatio-temporal patterns of dendritic voltages or intracellularions) to neuronal structure, during the very limited duration of an acute experiment.

This plugin tags all pixel/voxels in a skeleton image and then counts all its junctions, triple and quadruple points and branches, and measures their average and maximum length.

Tags are shown in a new window displaying every tag in a different color. You can find it under [Plugins>Skeleton>Analyze Skeleton (2D/3D)]. See Skeletonize3D for an example of how to produce skeleton images.

The voxels are classified into three different categories depending on their 26 neighbors: - End-point voxels: if they have less than 2 neighbors. - Junction voxels: if they have more than 2 neighbors. - Slab voxels: if they have exactly 2 neighbors.

End-point voxels are displayed in blue, slab voxels in orange and junction voxels in purple.

Notice here that, following this notation, the number of junction voxels can be different from the number of actual junctions since some junction voxels can be neighbors of each other.

Output data type: table result, image of the skeleton

SOAX is an open source software tool to extract the centerlines, junctions and filament lengths of biopolymer networks in 2D and 3D images. It facilitates quantitative, reproducible and objective analysis of the image data. The underlying method of SOAX uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then stretch along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments.

SOAX provides 3D visualization for exploring image data and visually checking results against the image. Quantitative analysis functions based on extracted networks are also implemented in SOAX, including spatial distribution, orientation, and curvature of filamentous structures. SOAX also provides interactive manual editing to further improve the extraction results, which can be saved in a file for archiving or further analysis. Useful for microtubules or actin filaments.

Observation: Depending on the operating system, the installation may or may not require Boost C++, ITK and VTK libraries. Windows has a standalone executable application without the need of those.